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Bug fix when running UG in GenotypeGivenAlleles mode: if an input site to genotype had no coverage, the output VCF had AC,AF and AN inherited from input VCF, which could have nothing to do with given BAM so numbers could be non-sensical. Now new vc has clear attributes instead of attributes inherited from input VCF.

This commit is contained in:
Guillermo del Angel 2012-02-06 11:58:13 -05:00
parent 090d87b48b
commit 827be878b4
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
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@ -252,7 +252,7 @@ public class UnifiedGenotyperEngine {
VariantContext vcInput = UnifiedGenotyperEngine.getVCFromAllelesRod(tracker, ref, rawContext.getLocation(), false, logger, UAC.alleles);
if ( vcInput == null )
return null;
vc = new VariantContextBuilder(vcInput).source("UG_call").noID().referenceBaseForIndel(ref.getBase()).make();
vc = new VariantContextBuilder(vcInput).source("UG_call").noID().referenceBaseForIndel(ref.getBase()).attributes(new HashMap<String, Object>()).make();
} else {
// deal with bad/non-standard reference bases
if ( !Allele.acceptableAlleleBases(new byte[]{ref.getBase()}) )